What if you used a search alert instead of a list alert. Could you make a search that returns just the docx files in a doc lib? if so create an alert on that search and see if it does the trick?
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ghangasFeb 18 '13 at 17:25

I went through this process myself (as you may have seen from my answer to your other question here)

Basically, alert views can't be based on certain default content types. My full adventure figuring that out, as well as a work-around and some potentially helpful code, is here for those who are curious. It involves creating a custom content type based on the folder and changing all folders to that new content type, then filtering based on it.